Search Results

What databases are available for Blast searches?

There are no Blast databases available on the helix systems. Blast searches are available to helix users, but are actually run at NCBI, National Library of Medicine on their Blast databases. NCBI maintains a list of databases available for Blast searches. As of Jun 1997, the following are available, but check their web page for changes/updates.

Peptide Sequence Databases
nr All non-redundant GenBank CDS translations+PDB+SwissProt+PIR
month All new or revised GenBank CDS translation+PDB+SwissProt+PIR released in the last 30 days.
swissprot the last major release of the SWISS-PROT protein sequence database (no updates)
yeast Yeast (Saccharomyces cerevisiae) protein sequences.
E. coli E. coli genomic CDS translations
pdb Sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank
kabat [kabatpro] Kabat's database of sequences of immunological interest
alu Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994) .
Nucleotide Sequence Databases
nr All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or HTGS sequences)
month All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days.
dbest Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions
dbsts Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions
htgs High Throughput Genomic Sequences
yeast Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences
E. coli E. coli genomic nucleotide sequences
pdb Sequences derived from the 3-dimensional structure
kabat [kabatnuc] Kabat's database of sequences of immunological interest
vector Vector subset of GenBank(R), NCBI, (anonymous FTP to ncbi.nlm.nih.gov beneath the /pub/vector directory)
mito Database of mitochondrial sequences, Rel. 1.0, July 1995"
alu Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994).
epd Eukaryotic Promotor Database
gss Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.

Peptide Sequence Databases
nr	All non-redundant GenBank CDS translations+PDB+SwissProt+PIR
month	All new or revised GenBank CDS translation+PDB+SwissProt+PIR released in the last 30 days.
swissprot	the last major release of the SWISS-PROT protein sequence database (no updates)
yeast	Yeast (Saccharomyces cerevisiae) protein sequences.
E. coli	E. coli genomic CDS translations
pdb	Sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank
kabat [kabatpro]	Kabat's database of sequences of immunological interest
alu	Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994) .
Nucleotide Sequence Databases
nr	All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or HTGS sequences)
month	All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days.
dbest	Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions
dbsts	Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions
htgs	High Throughput Genomic Sequences
yeast	Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences
E. coli	E. coli genomic nucleotide sequences
pdb	Sequences derived from the 3-dimensional structure
kabat [kabatnuc]	Kabat's database of sequences of immunological interest
vector	Vector subset of GenBank(R), NCBI, (anonymous FTP to ncbi.nlm.nih.gov beneath the /pub/vector directory)
mito	Database of mitochondrial sequences, Rel. 1.0, July 1995"
alu	Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994).
epd	Eukaryotic Promotor Database
gss	Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.